NOTE ON THE UNITS: CP2K USES SO CALLED “atomic units”. Meaning that the resulting energies are expressed in Hartree,
1 Hartree=27.2114 eV.
In the input file, the epsilon value (depth of the well) is expressed in KT units, namely, in “temperature” units (there is a Boltzmann constant K_b to make units work…).

1 Kelvin*K_b=3.2E-6 Hartree

. Using this conversion factor you can transform the epsilon value into Hartree, and the total energy can be expressed in units of epsilon. The sigma value is in Angstrom.

Do the same with ico.xyz which represents the icosahedral structure. You can look at all files with vmd.

extract the q4 order parameter from fcc.xyz and from fcc_rand.xyz and compare the values.

python stein.py file.xyz

You will be asked the cutoff radius for the neighbors, it is 1.391 in sigma units. You should input it in Angstrom. You will also be asked “value of l” This means the symmetry of the order parameter, which is l=4 in this case.

before running the simulation, copy the input coordinate file into in.xyz

cp fcc_rand.xyz in.xyz

Before running cp2k, check if the file OPT-pos-1.xyz is already present from a previous run. In that case remove or delete it accordingly. It contains the trajectory of the optimization.

run cp2k

cp2k.ssmp -i geo_opt.inp | tee geo_opt.out

(to see the output on the screen as well), or AS AN ALTERNATIVE

cp2k.ssmp -i geo_opt.inp > geo_opt.out

(to retain the output in the geo_opt.out file only)

in the output file, grep the final energy

grep "ENERGY|“ geo_opt.out

and transform it in the unit of the paper (epsilon units)

Open vmd and play with the optimization trajectory

vmd OPT-pos-1.xyz

(ask the teacher)

apply the script myq4 to the optimization trajectory: this generates a list of q4 and energies for the whole trajectory.

./myq4 OPT-pos-1.xyz > fcc.ene.q4

plot q4 and energies with gnuplot (ask the teacher)

have a look at the myq4 script

nano myq4

repeat for the ico.xyz starting point, don't forget to first copy/remove the files appropriately. For example:

mkdir FCC ; mv OPT* FCC ; mv geo_opt.out FCC

Run the bash script

./curve

Look inside, and try to understand what you get.

create a FCC_OUT subdirectory (mkdir FCC_OUT ; cd FCC_OUT) and copy there the files you want to keep; then go back one dir (cd ..), delete all the OPT* files (rm OPT* ) and repeat the exercise with ico.xyz

Assignment:

Report the energy of the minima, compare it with the ones of the initial configurations.

After converting the energy into “epsilon” units, estimate the number of bonds in the cluster, assuming a pairwise interaction.

Plot q4 vs. energy and q4 vs. optimization steps, for the two cases. Discuss the results. Are the minima in two separate basins?

Report the value of the order parameter of the minumum, and discuss what you see

Use “gnuplot” to make the output of “./curve” understandable, discuss the results.